Here's an interview from scifi.com that has a brief explanation about Eko's death.

Lost Producers Explain Death

Lost executive producers Carlton Cuse and Damon Lindelof told TV Guide's Michael Ausiello that this week's death of a major character was planned all along. (Spoilers ahead!) In the Nov. 1 episode, Mr. Eko (Adewale Akinnuoye-Agbaje) met his demise in the clutches of the mysterious smoke monster.

Cuse told Ausiello that Mr. Eko was never long for this world. "When Adewale came on the show, he didn't want to make a long-term commitment to a series," Cuse said. "We love him, and so we agreed that he would come on the show, and then we would find a time in which his arc would come to an end. And we sort of felt after a lot of conversations with him—most of which took place at the end of the spring last year—that we would finish his character somewhere in [these first] six episodes. And as we started talking about what was going to really help the drama of these six episodes, we thought, 'Well, this is the perfect place to do it.' As we said, we all kind of went into this [with the idea] that it was only going to be for a limited period of time."

As for rumors that Akinnuoye-Agbaje had strained relations with the rest of the cast and crew? "We don't really talk about anything other than the creative decisions made on the show," Lindelof said. "If you're hearing it from other people, you're not hearing that from us. Not to mention, we're in L.A. So we would never let that kind of thing determine the creative direction of the show. We're all in the service of the story." Lost winds up its first six episodes of the season on Nov. 8 before taking a 13-week hiatus. It airs Wednesdays at 9 p.m. PT/ET.